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PDBsum entry 1gvh
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Oxidoreductase
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PDB id
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1gvh
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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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The X-Ray structure of ferric escherichia coli flavohemoglobin reveals an unexpected geometry of the distal heme pocket.
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Authors
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A.Ilari,
A.Bonamore,
A.Farina,
K.A.Johnson,
A.Boffi.
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Ref.
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J Biol Chem, 2002,
277,
23725-23732.
[DOI no: ]
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PubMed id
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Abstract
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The x-ray structure of ferric unliganded lipid-free Escherichia coli
flavohemoglobin has been solved to a resolution of 2.2 A and refined to an
R-factor of 19%. The overall fold is similar to that of ferrous lipid-bound
Alcaligenes eutrophus flavohemoglobin with the notable exception of the E helix
positioning within the globin domain and a rotation of the NAD binding module
with respect to the FAD-binding domain accompanied by a substantial
rearrangement of the C-terminal region. An inspection of the heme environment in
E. coli flavohemoglobin reveals an unexpected architecture of the distal pocket.
In fact, the distal site is occupied by the isopropyl side chain Leu-E11 that
shields the heme iron from the residues in the topological positions predicted
to interact with heme iron-bound ligands, namely Tyr-B10 and Gln-E7, and
stabilizes a pentacoordinate ferric iron species. Ligand binding properties are
consistent with the presence of a pentacoordinate species in solution as
indicated by a very fast second order combination rates with imidazole and
azide. Surprisingly, imidazole, cyanide, and azide binding profiles at
equilibrium are not accounted for by a single site titration curve but are
biphasic and strongly suggest the presence of two distinct conformers within the
liganded species.
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Figure 3.
Fig. 3. Structural overlay of the globin domains of E.
coli and A. eutrophus flavohemoglobin and Vitreoscilla sp.
hemoglobin. The overlay among globin domains was obtained by
minimizing the C-  distances
for each protein using the program SEQUOIA (21) and was depicted
with the program MOLSCRIPT (28). The stereo diagram of the
globin domain of HMP ( red ribbons, yellow heme) is overlaid
with the corresponding domain of A. eutrophus flavohemoglobin
(green ribbons, green heme) in A and with Vitreoscilla Hb (cyan
ribbons, blue heme) in B.
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Figure 4.
Fig. 4. Structural details of the heme pocket in E. coli
ferric unliganded flavohemoglobin. The heme molecule is shown in
stereo together with a selection of amino acid residues within
the pocket at 5 Å from the macrocycle. The phenolic ring
of Tyr29-B10 located at >5 Å from the heme is also shown,
whereas the Phe^43-CD1 is hidden for clarity. The picture was
obtained with the program MOLSCRIPT (28).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2002,
277,
23725-23732)
copyright 2002.
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