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PDBsum entry 2nap
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Oxidoreductase
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PDB id
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2nap
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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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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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Abstract
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BACKGROUND: The periplasmic nitrate reductase (NAP) from the sulphate reducing
bacterium Desulfovibrio desulfuricans ATCC 27774 is induced by growth on nitrate
and catalyses the reduction of nitrate to nitrite for respiration. NAP is a
molybdenum-containing enzyme with one bis-molybdopterin guanine dinucleotide
cluster in a single polypeptide chain of 723
amino acid residues. To date, there is no crystal structure of a nitrate
reductase. RESULTS: The first crystal structure of a dissimilatory (respiratory)
nitrate reductase was determined at 1.9 A resolution by multiwavelength
anomalous diffraction (MAD) methods. The structure is folded into four domains
with an alpha/beta-type topology and all four domains are involved in cofactor
centre is located near the periphery of the molecule,
whereas the MGD cofactor extends across the interior of the molecule interacting
with residues from all four domains. The molybdenum atom is located at the
cluster.
The structure of NAP reveals the details of the catalytic molybdenum site, which
is coordinated to two MGD cofactors, Cys140, and a water/hydroxo ligand. A
facile electron-transfer pathway through bonds connects the molybdenum and the
cluster. CONCLUSIONS: The polypeptide fold of NAP and the arrangement
of the cofactors is related to that of Escherichia coli formate dehydrogenase
(FDH) and distantly resembles dimethylsulphoxide reductase. The close structural
homology of NAP and FDH shows how small changes in the vicinity of the
molybdenum catalytic site are sufficient for the substrate specificity.
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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
reprinted
by permission from Cell Press:
Structure
(1999,
7,
65-79)
copyright 1999.
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