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PDBsum entry 1qdb
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Oxidoreductase
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PDB id
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1qdb
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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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Structure of cytochrome c nitrite reductase.
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Authors
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O.Einsle,
A.Messerschmidt,
P.Stach,
G.P.Bourenkov,
H.D.Bartunik,
R.Huber,
P.M.Kroneck.
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Ref.
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Nature, 1999,
400,
476-480.
[DOI no: ]
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PubMed id
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Abstract
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The enzyme cytochrome c nitrite reductase catalyses the six-electron reduction
of nitrite to ammonia as one of the key steps in the biological nitrogen cycle,
where it participates in the anaerobic energy metabolism of dissimilatory
nitrate ammonification. Here we report on the crystal structure of this enzyme
from the microorganism Sulfurospirillum deleyianum, which we solved by
multiwavelength anomalous dispersion methods. We propose a reaction scheme for
the transformation of nitrite based on structural and spectroscopic information.
Cytochrome c nitrite reductase is a functional dimer, with 10 close-packed haem
groups of type c and an unusual lysine-coordinated high-spin haem at the active
site. By comparing the haem arrangement of this nitrite reductase with that of
other multihaem cytochromes, we have been able to identify a family of proteins
in which the orientation of haem groups is conserved whereas structure and
function are not.
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Figure 1.
Figure 1: The nitrite reductase dimer. A front view with the
dimer axis orientated vertically, the five haems in each monomer
(white), the Ca^2+ ions (grey) and Lys 133 which coordinates the
active-site iron atom (yellow). In the right monomer, the
protein chain is coloured blue from the amino-terminal end to
red at the carboxy-terminal end, in the left monomer according
to secondary structure. The dimer interface is dominated by
three long  -helices
per monomer. All haems in the dimer are covalently attached to
the protein and their iron atoms are arranged almost in a plane
parallel to the plane of the paper.
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Figure 2.
Figure 2: Haem arrangement. The overall orientation
corresponds to Fig. 1, with the active site located at haem 1
and the line indicating the dimer interface. Haems in the left
monomer are numbered according to their attachment to the
protein chain. In the right monomer, the Fe–Fe distances
(å) between the haems are given. Haems 5 interact across
the dimer interface with a distance closer than haems 2 and 3
within each monomer.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(1999,
400,
476-480)
copyright 1999.
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