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PDBsum entry 1utb
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Transcription regulation
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PDB id
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1utb
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Development of a bacterial biosensor for nitrotoluenes: the crystal structure of the transcriptional regulator dntr.
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Authors
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I.A.Smirnova,
C.Dian,
G.A.Leonard,
S.Mcsweeney,
D.Birse,
P.Brzezinski.
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Ref.
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J Mol Biol, 2004,
340,
405-418.
[DOI no: ]
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PubMed id
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Abstract
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The transcriptional regulator DntR, a member of the LysR family, is a central
element in a prototype bacterial cell-based biosensor for the detection of
hazardous contamination of soil and groundwater by dinitrotoluenes. To optimise
the sensitivity of the biosensor for such compounds we have chosen a rational
design of the inducer-binding cavity based on knowledge of the three-dimensional
structure of DntR. We report two crystal structures of DntR with acetate
(resolution 2.6 angstroms) and thiocyanate (resolution 2.3 angstroms),
respectively, occupying the inducer-binding cavity. These structures allow for
the construction of models of DntR in complex with salicylate (Kd approximately
or = 4 microM) and 2,4-dinitrotoluene that provide a basis for the design of
mutant DntR with enhanced specificity for dinitrotoluenes. In both crystal
structures DntR crystallises as a homodimer with a "head-to-tail"
arrangement of monomers in the asymmetric unit. Analysis of the crystal
structure has allowed the building of a full-length model of DntR in its
biologically active homotetrameric form consisting of two
"head-to-head" dimers. The implications of this model for the
mechanism of transcription regulation by LysR proteins are discussed.
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Figure 5.
Figure 5. DntR–ligand interactions. Stereoviews showing
substrate–protein interactions for the acetate-bound crystals
(a) and for the models of DntR containing salicylate (b) and
2,4-DNT (c) in the inducer-binding cavities. The surface defined
by protein residues is shown in light purple. Both side-chain
and main-chain atoms of amino acid residues that line the
inducer-binding cavity are shown in ball-and-stick
representation with carbon atoms coloured grey, oxygen atoms red
and nitrogen atoms blue. Acetate, salicylate and 2,4-DNT are
also shown in ball-and-stick mode with carbon atoms coloured
yellow, oxygen atoms red and nitrogen atoms blue. Water
molecules are shown as red spheres. Direct and water-mediated
hydrogen bonding interactions are shown as green and yellow
broken lines, respectively.
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Figure 6.
Figure 6. The DntR homotetramer. (a) A ribbon
representation of the homotetramer of DntR. The two molecules
that make up the dimer in the asymmetric unit of the DntR
crystals are shown in red and blue, respectively. The arrows
indicate the position of the linker helices of the monomers B.
The homotetramer is the result of the interaction of two
homodimers related by a crystallographic symmetry such that the
two dimers that constitute the homotetramer have co-ordinates
(x, y, z) and (1−x, y, 1/2−z).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2004,
340,
405-418)
copyright 2004.
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