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PDBsum entry 1dp8
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Oxygen storage/transport
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PDB id
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1dp8
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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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New mechanistic insights from structural studies of the oxygen-Sensing domain of bradyrhizobium japonicum fixl.
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Authors
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W.Gong,
B.Hao,
M.K.Chan.
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Ref.
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Biochemistry, 2000,
39,
3955-3962.
[DOI no: ]
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PubMed id
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Abstract
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The FixL heme domain serves as the dioxygen switch in the FixL/FixJ
two-component system of Rhizobia. Recent structural studies of the
Bradyrhizobium japonicum FixL heme domain (BjFixLH) have suggested an allosteric
mechanism that is distinct from the classical hemoglobin model. To gain further
insight into the FixL sensing mechanism, structures of BjFixLH bound to
dioxygen, imidazole, and nitric oxide have been determined. These structures,
particularly the structure of BjFixLH bound to its physiological ligand,
dioxygen, have helped to address a number of important issues relevant to the
BjFixLH sensing mechanism. On the basis of the oxy-BjFixLH structure, a
conserved arginine is found to stabilize the dioxygen ligand in a mode
reminiscent of the distal histidine in classical myoglobins and hemoglobins. The
structure of BjFixLH bound to imidazole elucidates the structural requirements
for accommodating sterically bulky ligands. Finally, the structure of BjFixLH
bound to nitric oxide provides evidence for a structural intermediate in the
heme-driven conformational change.
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Secondary reference #1
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Title
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Structure of a biological oxygen sensor: a new mechanism for heme-Driven signal transduction.
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Authors
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W.Gong,
B.Hao,
S.S.Mansy,
G.Gonzalez,
M.A.Gilles-Gonzalez,
M.K.Chan.
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Ref.
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Proc Natl Acad Sci U S A, 1998,
95,
15177-15182.
[DOI no: ]
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PubMed id
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Figure 3.
Fig. 3. Ball-and-stick diagrams of three heme-binding
pockets. Structures are shown for Glycera dibranchiata
hemoglobin (PDB ID: 2HBG) (Left), BjFixLH (Center), and the NO
transporter protein (PDB ID: 1NP1) (Right) (27, 28). The
rightmost and leftmost side chains correspond to the E7 and E11
residues of hemoglobins, respectively. The additional side chain
in BjFixLH (red) corresponds to Ile 215. The structures were
aligned based on the orientation of the proximal histidine and
the porphyrin ring. The atoms are colored as in Fig. 1.
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Figure 5.
Fig. 5. Comparison of the structures of the regulatory FG
loop of BjFixLH in the unliganded "on" and cyanide bound "off"
states. (A) The structure of the FG loop in the met-BjFixLH
(brown) illustrating the hydrogen-bonding interactions (Left)
and 2F[O]-F[C] electron density map (1  ) (Right).
(B) Corresponding figure for cyanomet-BjFixLH (blue) showing
hydrogen bonding (Left) and electron density (Right). (C)
Stereoview of overlap of the refined models for both states.
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