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PDBsum entry 1nir
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Nitrite reductase
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PDB id
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1nir
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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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N-Terminal arm exchange is observed in the 2.15 a crystal structure of oxidized nitrite reductase from pseudomonas aeruginosa.
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Authors
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D.Nurizzo,
M.C.Silvestrini,
M.Mathieu,
F.Cutruzzolà,
D.Bourgeois,
V.Fülöp,
J.Hajdu,
M.Brunori,
M.Tegoni,
C.Cambillau.
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Ref.
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Structure, 1997,
5,
1157-1171.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: Nitrite reductase from Pseudomonas aeruginosa (NiR-Pa) is a dimer
consisting of two identical 60 kDa subunits, each of which contains one c and
one d1 heme group. This enzyme, a soluble component of the electron-transfer
chain that uses nitrate as a source of energy, can be induced by the addition of
nitrate to the bacterial growth medium. NiR-Pa catalyzes the reduction of
nitrite (NO2-) to nitric oxide (NO); in vitro, both cytochrome c551 and azurin
are efficient electron donors in this reaction. NiR is a key denitrification
enzyme, which controls the rate of the production of toxic nitric oxide (NO) and
ultimately regulates the release of NO into the atmosphere. RESULTS: The
structure of the orthorhombic form (P2(1)2(1)2) of oxidized NiR-Pa was solved at
2.15 A resolution, using molecular replacement with the coordinates of the NiR
from Thiosphaera pantotropha (NiR-Tp) as the starting model. Although the
d1-heme domains are almost identical in both enzyme structures, the c domain of
NiR-Pa is more like the classical class I cytochrome-c fold because it has His51
and Met88 as heme ligands, instead of His17 and His69 present in NiR-Tp. In
addition, the methionine-bearing loop, which was displaced by His17 of the
NiR-Tp N-terminal segment, is back to normal in our structure. The N-terminal
residues (5/6-30) of NiR-Pa and NiR-Tp have little sequence identity. In Nir-Pa,
this N-terminal segment of one monomer crosses the dimer interface and wraps
itself around the other monomer. Tyr10 of this segment is hydrogen bonded to an
hydroxide ion--the sixth ligand of the d1-heme Fe, whereas the equivalent
residue in NiR-Tp, Tyr25, is directly bound to the Fe. CONCLUSIONS: Two ligands
of hemes c and d1 differ between the two known NiR structures, which accounts
for the fact that they have quite different spectroscopic and kinetic features.
The unexpected domain-crossing by the N-terminal segment of NiR-Pa is comparable
to that of 'domain swapping' or 'arm exchange' previously observed in other
systems and may explain the observed cooperativity between monomers of dimeric
NiR-Pa. In spite of having similar sequence and fold, the different kinetic
behaviour and the spectral features of NiR-Pa and NiR-Tp are tuned by the
N-terminal stretch of residues. A further example of this may come from another
NiR, from Pseudomonas stutzeri, which has an N terminus very different from that
of the two above mentioned NiRs.
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Figure 6.
Figure 6. Water-accessible surface area of NiR-Pa monomer
A, slabbed at the level of the d[1] heme. Water molecules are
colored in blue, the d[1] heme in red and the phosphate ion in
green. The channel starting from the d[1] heme and leading to
the `back door' is located between the d[1] heme and the
phosphate ion.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1997,
5,
1157-1171)
copyright 1997.
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