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PDBsum entry 1v5h
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Oxygen storage/transport
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PDB id
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1v5h
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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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Structural basis of human cytoglobin for ligand binding.
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Authors
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H.Sugimoto,
M.Makino,
H.Sawai,
N.Kawada,
K.Yoshizato,
Y.Shiro.
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Ref.
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J Mol Biol, 2004,
339,
873-885.
[DOI no: ]
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PubMed id
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Abstract
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Cytoglobin (Cgb), a newly discovered member of the vertebrate globin family,
binds O(2) reversibly via its heme, as is the case for other mammalian globins
(hemoglobin (Hb), myoglobin (Mb) and neuroglobin (Ngb)). While Cgb is expressed
in various tissues, its physiological role is not clearly understood. Here, the
X-ray crystal structure of wild type human Cgb in the ferric state at 2.4A
resolution is reported. In the crystal structure, ferric Cgb is dimerized
through two intermolecular disulfide bonds between Cys38(B2) and Cys83(E9), and
the dimerization interface is similar to that of lamprey Hb and Ngb. The overall
backbone structure of the Cgb monomer exhibits a traditional globin fold with a
three-over-three alpha-helical sandwich, in which the arrangement of helices is
basically the same among all globins studied to date. A detailed comparison
reveals that the backbone structure of the CD corner to D helix region, the N
terminus of the E-helix and the F-helix of Cgb resembles more closely those of
pentacoordinated globins (Mb, lamprey Hb), rather than hexacoordinated globins
(Ngb, rice Hb). However, the His81(E7) imidazole group coordinates directly to
the heme iron as a sixth axial ligand to form a hexcoordinated heme, like Ngb
and rice Hb. The position and orientation of the highly conserved residues in
the heme pocket (Phe(CD1), Val(E11), distal His(E7) and proximal His(F8)) are
similar to those of other globin proteins. Two alternative conformations of the
Arg84(E10) guanidium group were observed, suggesting that it participates in
ligand binding to Cgb, as is the case for Arg(E10) of Aplysia Mb and Lys(E10) of
Ngb. The structural diversities and similarities among globin proteins are
discussed with relevance to molecular evolutionary relationships.
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Figure 1.
Figure 1. Stereo diagram of the final electron density map
around the heme of Cgb from (a) parallel with the heme plane and
(b) distal side of heme plane. The sigmaA[57.] weighted 2mF[o]
-DF[c] map is contoured at the 1.1s level. The final refined
coordinates for Cgb are superimposed. Oxygen and nitrogen atoms
are coloured red and blue, respectively. The distal and proximal
His and heme are coloured in gold stick. Other residues are in
gray stick. The imidazole groups of His81(E7) and His113(F8)
bind to the heme iron as endogenous axial ligands to form the
hexacoordinated structure. The iron-bound imidazole of distal
His81(E7) is surrounded by Phe60(CD1) and Val85(E11), which are
located on the porphyrin pyrrols D and B, respectively.
Arg84(E10) in the distal side is also close the heme and
exhibits alternative conformations. The Figure was prepared with
program O.[51.]
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Figure 7.
Figure 7. Comparison of the CD, D, E and F helices regions.
The 33 atoms in the heme plane were used in the least-squares
fitting. Cgb (green) is superimposed on (a) Mb (blue), (b) rice
Hb (gray), (c) Ngb (orange) or (d) sea lamprey Hb (red). The
distal and proximal His and heme are represented by a stick
model.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2004,
339,
873-885)
copyright 2004.
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Secondary reference #1
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Title
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Characterization of the heme environmental structure of cytoglobin, A fourth globin in humans.
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Authors
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H.Sawai,
N.Kawada,
K.Yoshizato,
H.Nakajima,
S.Aono,
Y.Shiro.
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Ref.
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Biochemistry, 2003,
42,
5133-5142.
[DOI no: ]
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PubMed id
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