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PDBsum entry 2fmy
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DNA binding protein
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PDB id
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2fmy
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References listed in PDB file
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Key reference
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Title
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Crystal structure of co-Sensing transcription activator cooa bound to exogenous ligand imidazole.
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Authors
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H.Komori,
S.Inagaki,
S.Yoshioka,
S.Aono,
Y.Higuchi.
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Ref.
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J Mol Biol, 2007,
367,
864-871.
[DOI no: ]
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PubMed id
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Abstract
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CooA is a CO-dependent transcriptional activator and transmits a CO-sensing
signal to a DNA promoter that controls the expression of the genes responsible
for CO metabolism. CooA contains a b-type heme as the active site for sensing
CO. CO binding to the heme induces a conformational change that switches CooA
from an inactive to an active DNA-binding form. Here, we report the crystal
structure of an imidazole-bound form of CooA from Carboxydothermus
hydrogenoformans (Ch-CooA). In the resting form, Ch-CooA has a six-coordinate
ferrous heme with two endogenous axial ligands, the alpha-amino group of the
N-terminal amino acid and a histidine residue. The N-terminal amino group of
CooA that is coordinated to the heme iron is replaced by CO. This substitution
presumably triggers a structural change leading to the active form. The crystal
structure of Ch-CooA reveals that imidazole binds to the heme, which replaces
the N terminus, as does CO. The dissociated N terminus is positioned
approximately 16 A from the heme iron in the imidazole-bound form. In addition,
the heme plane is rotated by 30 degrees about the normal of the porphyrin ring
compared to that found in the inactive form of Rhodospirillum rubrum CooA. Even
though the ligand exchange, imidazole-bound Ch-CooA remains in the inactive form
for DNA binding. These results indicate that the release of the N terminus
resulting from imidazole binding is not sufficient to activate CooA. The
structure provides new insights into the structural changes required to achieve
activation.
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Figure 2.
Figure 2. Stereo view of a ball- and -stick model of the heme
and some residues with Im-omitted F[o]–F[c] map. The map is
shown in green and contoured at 5σ. The heme exists in a
six-coordinate form with His82 and Im ligands. Im is located in
the hydrophobic pocket formed by the C-helix and the N-terminal
region (from M5 to L7). The N-terminal amino group (N) of
Im-bound Ch-CooA is located 16 Å from the heme iron.
Carbon, nitrogen, oxygen and sulfur atoms are shown in grey,
blue, red and yellow, respectively.
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Figure 3.
Figure 3. Comparison of the heme orientation of Ch-CooA
(green) and Rr-CooA (cyan). His82 of Ch-CooA and His77 of
Rr-CooA are superimposed. The meso α–γ axis is shown as a
dotted line. The heme is rotated by  vert,
similar 30° about the normal of the heme plane in Im-bound
Ch-CooA relative to Rr-CooA. In Im-bound Ch-CooA, the heme
propionates interact with Lys194 in the DNA-binding domain and
Arg84 in the effector-binding domain, while the heme propionate
of Rr-CooA interacts with Arg4 in the N-terminal region.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2007,
367,
864-871)
copyright 2007.
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