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PDBsum entry 1ogy
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Oxidoreductase
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PDB id
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1ogy
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Contents |
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(+ 2 more)
790 a.a.
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(+ 2 more)
127 a.a.
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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 and redox plasticity in the heterodimeric periplasmic nitrate reductase.
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Authors
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P.Arnoux,
M.Sabaty,
J.Alric,
B.Frangioni,
B.Guigliarelli,
J.M.Adriano,
D.Pignol.
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Ref.
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Nat Struct Biol, 2003,
10,
928-934.
[DOI no: ]
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PubMed id
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Abstract
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The structure of the respiratory nitrate reductase (NapAB) from Rhodobacter
sphaeroides, the periplasmic heterodimeric enzyme responsible for the first step
in the denitrification process, has been determined at a resolution of 3.2 A.
The di-heme electron transfer small subunit NapB binds to the large subunit with
cluster of NapA. A total of 57
residues at the N- and C-terminal extremities of NapB adopt an extended
conformation, embracing the NapA subunit and largely contributing to the total
area of 5,900 A(2) buried in the complex. Complex formation was studied further
by measuring the variation of the redox potentials of all the cofactors upon
binding. The marked effects observed are interpreted in light of the
three-dimensional structure and depict a plasticity that contributes to an
efficient electron transfer in the complex from the heme I of NapB to the
molybdenum catalytic site of NapA.
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Figure 1.
Figure 1. Stereo views of the overall fold of the NapAB complex.
(a) NapA is represented as a white ribbon, and NapB is
colored from blue to red from the N to the C terminus,
respectively. Molybdenum and iron atoms are represented as CPK
models. (b) The same view as in a, rotated by 90°. NapB is
white. The four structural domains of NapA are colored as
follows: domain I, red; domain II, green; domain III, yellow;
domain IV, blue. Domain definitions were taken from Dias et al9.
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Figure 2.
Figure 2. Comparisons of NapAB complex with the structures of
the uncomplexed subunits. (a) Ribbon diagram of the NapAB
complex. NapA is colored according to the r.m.s. deviations
obtained by a superposition with the structure of the monomeric
NapA from D. desulfuricans: residues with r.m.s. deviation <1.5
Å are in gold, between 1.5 and 2 Å in orange and >2.0 Å in red.
Sequence insertions are green. The NapB subunit is blue. (b)
Superimposition of the NapAB structure (NapB is colored in red
with the hemes in light colors, and the NapA subunit is
represented according to its surface) with the structure of the
proteolytic fragment of NapB from H. influenzae (in green with
the hemes in dark colors).
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2003,
10,
928-934)
copyright 2003.
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Secondary reference #1
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Title
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The 1.25 a resolution structure of the diheme napb subunit of soluble nitrate reductase reveals a novel cytochrome c fold with a stacked heme arrangement.
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Authors
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A.Brigé,
D.Leys,
T.E.Meyer,
M.A.Cusanovich,
J.J.Van beeumen.
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Ref.
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Biochemistry, 2002,
41,
4827-4836.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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Crystal structure of the first dissimilatory nitrate reductase at 1.9 a solved by mad methods.
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Authors
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J.M.Dias,
M.E.Than,
A.Humm,
R.Huber,
G.P.Bourenkov,
H.D.Bartunik,
S.Bursakov,
J.Calvete,
J.Caldeira,
C.Carneiro,
J.J.Moura,
I.Moura,
M.J.Romão.
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Ref.
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Structure, 1999,
7,
65-79.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. The overall fold of NAP. (a) Stereoview of the
structure of NAP from Desulfovibrio desulfuricans ATCC 27774
with the different domains coloured: domain I (residues 4–61,
464–492 and 517–561) in red; domain II (residues 62–135,
347–463 and 493–516) in green; domain III (residues
136–346) in yellow; and domain IV (residues 562–723) in
blue. The funnel-like cavity, which provides access to the
molybdenum catalytic site, can be seen on the upper part of the
molecule between domains II and III. (b) Stereoview Cα trace
of NAP for domains I and III with residues labelled. (c)
Stereoview Cα trace of NAP for domains II and IV with residues
labelled. The MGD cofactors and the [4Fe–4S] cluster are shown
in ball-and-stick representation. (Figures were prepared with
the programs MOLSCRIPT [75] and Raster-3D [76].)
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The above figure is
reproduced from the cited reference
with permission from Cell Press
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