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PDBsum entry 2an7
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DNA binding protein
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PDB id
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2an7
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References listed in PDB file
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Key reference
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Title
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The solution structure of pard, The antidote of the parde toxin antitoxin module, Provides the structural basis for DNA and toxin binding.
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Authors
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M.Oberer,
K.Zangger,
K.Gruber,
W.Keller.
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Ref.
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Protein Sci, 2007,
16,
1676-1688.
[DOI no: ]
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PubMed id
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Abstract
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ParD is the antidote of the plasmid-encoded toxin-antitoxin (TA) system
ParD-ParE. These modules rely on differential stabilities of a highly expressed
but labile antidote and a stable toxin expressed from one operon. Consequently,
loss of the coding plasmid results in loss of the protective antidote and
poisoning of the cell. The antidote protein usually also exhibits an
autoregulatory function of the operon. In this paper, we present the solution
structure of ParD. The repressor activity of ParD is mediated by the N-terminal
half of the protein, which adopts a ribbon-helix-helix (RHH) fold. The
C-terminal half of the protein is unstructured in the absence of its cognate
binding partner ParE. Based on homology with other RHH proteins, we present a
model of the ParD-DNA interaction, with the antiparallel beta-strand being
inserted into the major groove of DNA. The fusion of the N-terminal DNA-binding
RHH motif to the toxin-binding unstructured C-terminal domain is discussed in
its evolutionary context.
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Figure 1.
The experimentally derived restraints per residue reflect the
two-domain architecture of ParD protein. The shading is hatched,
light gray, dark gray, black, and dotted for intraresidue,
sequential, short-range (d[ij], j < i + 5), long-range (d[ij], j
> i + 4), and intermonomer NOEs, respectively.
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Figure 5.
Model of the ParD --DNA complex. The ParD --DNA complex is
shown in a ribbon presentation: (blue and light blue) the two
chains of the ParD dimer, and (green and pale green) the two
strands of the 10-bp inverted repeat. Residues involved in
protein --DNA interactions are shown in stick presentation:
(gray) those pointing into the major groove of the DNA (Arg3,
Thr5, and Asp7), (yellow) those interacting with the phosphate
backbone. (A) View along the [beta]-ribbon protruding the major
groove. (B) View approximately along the twofold axis of the
dimer. The line drawing of the nucleotides was omitted for
clarity. (C) The superposition of two ParD dimers with the MetJ
--DNA complex (PDB entry: 1mjo). The ParD dimers are shown as
ribbon drawing: (blue) chain A, (pale green) chain B, (pink) the
hydrophobic patches positioned at the dimer --dimer interface
above the minor groove. The DNA represents the original 19-mer
repressor site of MetJ (Garvie and Phillips 2000). (D) The ParD
promoter sequence from [minus sign]32 to +17, showing the
inverted repeat (solid boxes) and the flanking half sites (half
tone).
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The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(2007,
16,
1676-1688)
copyright 2007.
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Secondary reference #1
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Title
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The anti-Toxin pard of plasmid rk2 consists of two structurally distinct moieties and belongs to the ribbon-Helix-Helix family of DNA-Binding proteins.
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Authors
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M.Oberer,
K.Zangger,
S.Prytulla,
W.Keller.
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Ref.
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Biochem J, 2002,
361,
41-47.
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PubMed id
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