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PDBsum entry 1vxb
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Oxygen storage
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PDB id
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1vxb
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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 structures of co-, Deoxy- And met-Myoglobins at various ph values.
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Authors
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F.Yang,
G.N.Phillips.
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Ref.
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J Mol Biol, 1996,
256,
762-774.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
93%.
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Abstract
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The distal histidine residue, His64(E7), and the proximal histidine residue,
His93(F8), in myoglobin (Mb) are important for the function of the protein. For
example, the increase in the association rate constant for CO binding at low pH
has been suggested to be caused by the protonation of these histidine residues.
In order to investigate the influence of protonation on the structure of
myoglobin, we determined the crystal structures of sperm whale myoglobin to 2.0
A or better in different states of ligation (MbCO, deoxyMb and metMb) at pH
values of 4, 5 and 6. The most dramatic change found at low pH is that His64
swings out of the distal pocket in the MbCO structure at pH 4, opening a direct
channel from the solvent to the iron atom. This rotation seems to be facilitated
by conformational changes in the CD corner. The benzyl side-chain of Phe46(CD4),
which has been suggested to be a critical residue in controlling the rotation of
His64, moves away from His64 at pH 4 in the deoxyMb structure, allowing more
free rotation of His64. Arg45(CD3) is also important for the dynamics of
myoglobin, since it influences the pK(a) of His64 and forms a hydrogen bond
lattice that hinders the rotation of His64 at neutral pH. This hydrogen-bond
lattice disappears at low pH. Although His64 rotates out of the distal pocket in
the MbCO structure at pH 4, leaving more space for the CO ligand, the Fe-C-O
angle refines to about 130 degrees, the same as those at pH 5 and 6. In the MbCO
structure at pH 4, significant conformational changes appear in the EF corner.
The peptide plane between Lys79(EF2) and Gly80(EF3) flips about 150 degrees. The
occupancy of this conformation in the MbCO structures increases with decreases
in pH. On the proximal side of the heme, the bond between the heme iron atom and
N(epsilon) of His93 remains intact under the experimental conditions in the MbCO
and deoxyMb structures, but appears elongated in the metMb structure at pH 4,
representing either a weakened bond or the breakage of the bond in some fraction
of the molecules in the crystal.
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Figure 4.
Figure 4. The heme pocket of metMb at pH 4 (white), 5 (yellow) and 6 (red). On the distal side at pH 4, the movement
of the water molecule ligand and His64 is similar to that in the deoxyMb structure at pH 4 due to the protonation of
the group (Figure 1(b)). On the proximal side, His93 undergoes significant conformational changes and the distance
from the iron atom to N
e
of His93 is 2.5 Å , representing either a weakened bond or the breakage of the bond in some
molecules in the crystal. The =2Fo - Fc= electron density map is contoured at 1.5 standard deviations above the average
density of the map for metMb at pH 4.
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Figure 6.
Figure 6. The CD corner in deoxyMb at pH 4 (white), pH 5 (yellow) and pH 6 (red). Phe46 moves to the left in the
Figure at pH 4, increasing its distance to His64. N
d
of His48 hydrogen bonds to the carbonyl oxygen atom of Arg45
at pH 4, which may be the cause of the large displacement of these two residues. The rotation of the terminal atoms
of the side-chain of Arg45 at pH 4 disrupts the hydrogen-bond lattice. The heme-6-propionate group is in a new
conformation at pH 4, probably due to the loss of its hydrogen bond with Arg45. The =2Fo - Fc = electron density map
is contoured at 1.5 standard deviations above the average density of the map for deoxyMb at pH 4.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1996,
256,
762-774)
copyright 1996.
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Secondary reference #1
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Title
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X-Ray structure and refinement of carbon-Monoxy (fe ii)-Myoglobin at 1.5 a resolution.
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Authors
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J.Kuriyan,
S.Wilz,
M.Karplus,
G.A.Petsko.
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Ref.
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J Mol Biol, 1986,
192,
133-154.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2. The eme group, and eviations rom
planarity. The nomenclature used or he atoms f he
heme is shown. The eviations of atoms that eviate by
more han .1 A rom the plane of he 4 yrrole nitrogen
atoms in O-Mb re ndicated. he igures in arenthees
are he deviations for deoxy-Mb. The dihedral ngle q5
used to escribe the CO onformations is shown.
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Figure 7.
Figure 7. xl-x2 energy map for is64 7. The total
nergy s alculated as a functio of 1 and x2 with the
of the protein kept fixed. There are 10 contour levels
rom - 16 100.0 kcal/mol. (a) Arg45 CD3 is in
onformation A. The X-ray conformation of is64 E7 is
arked ith n X. b) Arg45 CD3 is in conformation B.
he conformation of His64 E7 t was used in
salculating the nergy map in Fig. 4(d) s mared with
n X.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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