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PDBsum entry 1q1f
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Oxygen storage/transport
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PDB id
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1q1f
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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 structure of murine neuroglobin: novel pathways for ligand migration and binding.
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Authors
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B.Vallone,
K.Nienhaus,
M.Brunori,
G.U.Nienhaus.
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Ref.
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Proteins, 2004,
56,
85-92.
[DOI no: ]
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PubMed id
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Abstract
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Neuroglobin, a recently discovered globin predominantly expressed in neuronal
tissue of vertebrates, binds small, gaseous ligands at the sixth coordination
position of the heme iron. In the absence of an exogenous ligand, the distal
histidine (His64) binds to the heme iron in the ferrous and ferric states. The
crystal structure of murine ferric (met) neuroglobin at 1.5 A reveals
interesting features relevant to the ligand binding mechanism. Only weak
selectivity is observed for the two possible heme orientations, the occupancy
ratio being 70:30. Two small internal cavities are present on the heme distal
side, which enable the His64(E7) side chain to move out of the way upon
exogenous ligand binding. Moreover, a third, huge cavity (volume approximately
290 A3) connecting both sides of the heme, is open towards the exterior and
provides a potential passageway for ligands. The CD and EF corners exhibit
substantial flexibility, which may assist ligands in entering the protein and
accessing the active site. Based on this high-resolution structure, further
structure-function studies can be planned to elucidate the role of neuroglobin
in physiological responses to hypoxia.
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Figure 4.
Figure 4. The different heme conformers of Ngb. Blue: conformer
A (70% occupancy). Red: conformer B (30%). Close distances are:
Tyr44(CD3)  OH
to heme propionate O2A
= 2.6 Å, heme propionate O2A
to Wat3 = 2.7 Å, Lys67(E10) NZ
to heme propionate O1A
= 2.7 Å.
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Figure 6.
Figure 6. Modeling dioxygen binding to the distal site of Ngb.
a: The original His64(E7) position (  [1]
= 178.1°) overlaps with the first atom of the diatomic
ligand (0.28 Å). b: His64(E7) swings towards the interior;
at [1]
= -72.5°, there are no close contacts of the imidazole side
chain with other amino acids or with the bound ligand. c:
His64(E7) swings towards the exterior; at [1]
= 114.5°, there is a steric clash with O2A of the heme
propionate (distance 0.63 Å) and close contact with
Tyr44(CD3)-OH (2.14 Å) and Wat3 (1.95 Å).
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2004,
56,
85-92)
copyright 2004.
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