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DOI no:
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J Biol Chem
279:20356-20362
(2004)
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PubMed id:
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The structural mechanism for transcription activation by MerR family member multidrug transporter activation, N terminus.
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K.J.Newberry,
R.G.Brennan.
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ABSTRACT
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Transcription regulators of the MerR family respond to myriad stress signals to
activate sigma70/sigmaA-targeted genes, which contain suboptimal 19-bp spacers
between their -35 and -10 promoter elements. The crystal structure of a
BmrR-TPP(+)-DNA complex provided initial insight into the transcription
activation mechanism of the MerR family, which involves base pair distortion,
DNA undertwisting and shortening of the spacer, and realignment of the -35 and
-10 boxes. Here, we describe the crystal structure of MerR family member MtaN
bound to the mta promoter. Although the global DNA binding modes of MtaN and
BmrR differ somewhat, homologous protein-DNA interactions are maintained.
Moreover, despite their different sequences, the mta promoter conformation is
essentially identical to that of the BmrR-TPP(+)-bound bmr promoter, indicating
that this DNA distortion mechanism is common to the entire MerR family.
Interestingly, DNA binding experiments reveal that the identity of the two
central bases of the mta and bmr promoters, which are conserved as either a
thymidine or an adenine in nearly all MerR promoters, is not important for DNA
affinity. Comparison of the free and DNA-bound MtaN structures reveals that a
conformational hinge, centered at residues N-terminal to the ubiquitous coiled
coil, is key for mta promoter binding. Analysis of the structures of BmrR, CueR,
and ZntR indicates that this hinge may be common to all MerR family members.
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Selected figure(s)
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Figure 4.
FIG. 4. Structural mechanism of transcription activation by
the MerR family. a, superimposition of the MtaN-DNA and
BmrRTPP+-DNA complexes. Helices 1 to 4 of one subunit from each
dimer, but not W1, were overlaid. Yellow, BmrR; blue, MtaN. b,
overlay of the MtaN-mta and BmrR-bmr promoter structures using
all equivalent phosphate backbone groups. Blue, mta DNA; yellow,
bmr DNA. c, close up of the superimposed mta and bmr promoters
near base pair 1. Notice their nearly identical structures at
the site of DNA distortion. Blue sticks, mta promoter DNA;
yellow sticks, bmr promoter DNA.
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Figure 5.
FIG. 5. Representative DNA binding isotherms. a,
equilibrium binding isotherm of BmrR titrated into bmrT[1]A[2]
DNA. To ensure equilibrium binding, 0.2 nM fluorescein-labeled
DNA was used in this experiment. b, equilibrium binding isotherm
of MtaN titrated into MtaN-mtaT[1']T[2'] DNA. To ensure
equilibrium binding, 1 nM fluorescein-labeled DNA was used in
this experiment. mP, millipolarization.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2004,
279,
20356-20362)
copyright 2004.
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Figures were
selected
by the author.
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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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C.H.Wu,
D.Le,
A.Mulchandani,
and
W.Chen
(2009).
Optimization of a whole-cell cadmium sensor with a toggle gene circuit.
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Biotechnol Prog, 25,
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A.A.Gorodetsky,
L.E.Dietrich,
P.E.Lee,
B.Demple,
D.K.Newman,
and
J.K.Barton
(2008).
DNA binding shifts the redox potential of the transcription factor SoxR.
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Proc Natl Acad Sci U S A, 105,
3684-3689.
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J.Zhao,
W.Niu,
J.Yao,
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E.M.Marcotte,
and
A.M.Lambowitz
(2008).
Group II intron protein localization and insertion sites are affected by polyphosphate.
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PLoS Biol, 6,
e150.
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K.J.Newberry,
J.L.Huffman,
M.C.Miller,
N.Vazquez-Laslop,
A.A.Neyfakh,
and
R.G.Brennan
(2008).
Structures of BmrR-drug complexes reveal a rigid multidrug binding pocket and transcription activation through tyrosine expulsion.
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J Biol Chem, 283,
26795-26804.
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PDB codes:
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S.A.Shelburne,
D.B.Keith,
M.T.Davenport,
N.Horstmann,
R.G.Brennan,
and
J.M.Musser
(2008).
Molecular characterization of group A Streptococcus maltodextrin catabolism and its role in pharyngitis.
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Mol Microbiol, 69,
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S.Watanabe,
A.Kita,
K.Kobayashi,
and
K.Miki
(2008).
Crystal structure of the [2Fe-2S] oxidative-stress sensor SoxR bound to DNA.
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Proc Natl Acad Sci U S A, 105,
4121-4126.
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PDB codes:
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G.Navarro-Avilés,
M.A.Jiménez,
M.C.Pérez-Marín,
C.González,
M.Rico,
F.J.Murillo,
M.Elías-Arnanz,
and
S.Padmanabhan
(2007).
Structural basis for operator and antirepressor recognition by Myxococcus xanthus CarA repressor.
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| |
Mol Microbiol, 63,
980-994.
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PDB code:
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L.V.Wray,
and
S.H.Fisher
(2007).
Functional analysis of the carboxy-terminal region of Bacillus subtilis TnrA, a MerR family protein.
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J Bacteriol, 189,
20-27.
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O.N.Oktyabrsky,
and
G.V.Smirnova
(2007).
Redox regulation of cellular functions.
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Biochemistry (Mosc), 72,
132-145.
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J.M.Zalieckas,
L.V.Wray,
and
S.H.Fisher
(2006).
Cross-regulation of the Bacillus subtilis glnRA and tnrA genes provides evidence for DNA binding site discrimination by GlnR and TnrA.
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J Bacteriol, 188,
2578-2585.
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J.Qiu,
D.Zhou,
L.Qin,
Y.Han,
X.Wang,
Z.DU,
Y.Song,
and
R.Yang
(2006).
Microarray expression profiling of Yersinia pestis in response to chloramphenicol.
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FEMS Microbiol Lett, 263,
26-31.
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M.Ventura,
C.Canchaya,
Z.Zhang,
V.Bernini,
G.F.Fitzgerald,
and
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(2006).
How high G+C Gram-positive bacteria and in particular bifidobacteria cope with heat stress: protein players and regulators.
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FEMS Microbiol Rev, 30,
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S.Watanabe,
A.Kita,
K.Kobayashi,
Y.Takahashi,
and
K.Miki
(2006).
Crystallization and preliminary X-ray crystallographic studies of the oxidative-stress sensor SoxR and its complex with DNA.
|
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Acta Crystallogr Sect F Struct Biol Cryst Commun, 62,
1275-1277.
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A.C.Hunt,
L.Servín-González,
G.H.Kelemen,
and
M.J.Buttner
(2005).
The bldC developmental locus of Streptomyces coelicolor encodes a member of a family of small DNA-binding proteins related to the DNA-binding domains of the MerR family.
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J Bacteriol, 187,
716-728.
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J.L.Hobman,
J.Wilkie,
and
N.L.Brown
(2005).
A design for life: prokaryotic metal-binding MerR family regulators.
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Biometals, 18,
429-436.
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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
codes are
shown on the right.
|
109 a.a.
